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Links tagged with 'forecasting'

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CIBEXDatabase Content

http://cibex.nig.ac.jp/ [open in a new window]

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Expression > Transcript Expression Analysis

The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.

links directory index: 226
TitlePublication YearGoogle Scholar Citation Count
Submission of microarray data to public repositories200494
CIBEX: center for information biology gene expression database2003132
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tagscomputational biology database management systems forecasting gene expression gene expression profiling genetic databases information systems oligonucleotide array sequence analysis software design

euGenes: Genomic Information for Eukaryotic OrganismsDatabase Content

http://iubio.bio.indiana.edu:8089/ [open in a new window]

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Model Organisms > General Resources

Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
euGenes: a eukaryote genome information system200239
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tagsanimals arabidopsis caenorhabditis elegans chromosome mapping database management systems drosophila forecasting genetic databases genome humans mice saccharomyces sequence homology zebrafish

Genome Biology Release 3 of the Drosophila genomeResource Content

http://genomebiology.com/series/drosophila [open in a new window]

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Model Organisms > Fly

A series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.

links directory index: 1971
TitlePublication YearGoogle Scholar Citation Count
Systematic determination of patterns of gene expression during Drosophila embryogenesis2002340
Computational analysis of core promoters in the Drosophila genome20023
Apollo: a sequence annotation editor2002279
An integrated computational pipeline and database to support whole-genome sequence annotation200241
A Drosophila full-length cDNA resource2002148
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence2002275
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome2002125
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly2002168
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective2002313
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review2002279
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tagsalgorithms amino acid sequence animals base composition base sequence cluster analysis complementary dna computational biology computer-assisted image processing conserved sequence contig mapping database management systems developmental gene expression regulation dna sequence analysis dna transposable elements drosophila drosophila melanogaster drosophila proteins euchromatin expressed sequence tags forecasting gene dosage gene expression profiling gene rearrangement genetic databases genetic promoter regions genetic variation genome heterochromatin humans in situ hybridization insect genes insertional mutagenesis messenger rna molecular evolution molecular sequence data multigene family nucleic acid conformation nucleic acid databases oligonucleotide array sequence analysis physical chromosome mapping protein databases research design software design software validation species specificity transcription initiation site untranslated regions x chromosome

GlyNest and CASPERTool Content

http://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation [open in a new window]

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Other Molecules > Carbohydrates

GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.

This content is being maintained by luetteke.

links directory index: 181
TitlePublication YearGoogle Scholar Citation Count
GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface200616
The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra200648
SWEET-DB: an attempt to create annotated data collections for carbohydrates200270
Computer-assisted structural analysis of oligo- and polysaccharides: an extension of CASPER to multibranched structures199827
CASPER: a computer program used for structural analysis of carbohydrates199120
NAR Web Server Issue 2006
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tagsalgorithms automatic data processing bacterial capsules bacterial polysaccharides biomolecular nuclear magnetic resonance carbohydrate conformation carbohydrate sequence carbohydrates carbon isotopes computational biology computer simulation factual databases forecasting glycopeptides glycoproteins hydrogen magnetic resonance spectroscopy molecular models molecular sequence data molecular structure o antigens oligosaccharides polysaccharides systems integration three-dimensional imaging

mirDIPDatabase Content

http://ophid.utoronto.ca/mirDIP/ [open in a new window]

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RNA > Databases
RNA > Functional RNAs

mirDIP integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs20118
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tagsalgorithms biological models cluster analysis computational biology forecasting human genome humans metabolic networks and pathways micrornas nucleic acid databases protein interaction mapping rna sequence analysis signal transduction validation studies as topic
setsUniversity of Toronto

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/ [open in a new window]

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Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

links directory index: 447
TitlePublication YearGoogle Scholar Citation Count
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information1996447
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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

PBETool Content

http://bioinformatics.univ-reunion.fr/PBE/ [open in a new window]

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Protein > 3-D Structure Comparison

Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.

links directory index: 252
TitlePublication YearGoogle Scholar Citation Count
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet200643
New assessment of a structural alphabet200541
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks2000168
NAR Web Server Issue 2006
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tagsamino acid motifs artificial intelligence bayes theorem cluster analysis computer simulation factual databases forecasting ligases molecular models neural networks (computer) peptide fragments protein conformation protein databases protein folding protein sequence analysis proteins secondary protein structure sequence alignment ubiquitins

SCORDatabase Content

http://scor.berkeley.edu/ [open in a new window]

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RNA > Functional RNAs
RNA > General Resources
RNA > Motifs

The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.

links directory index: 169
TitlePublication YearGoogle Scholar Citation Count
SCOR: Structural Classification of RNA, version 2.0200475
SCOR: a Structural Classification of RNA database200294
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tagsanimals base pairing biomolecular nuclear magnetic resonance computational biology conserved sequence forecasting humans nucleic acid conformation nucleic acid databases rna structure-activity relationship x-ray crystallography

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

links directory index: 984
TitlePublication YearGoogle Scholar Citation Count
TRAMPLE: the transmembrane protein labelling environment200510
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins2002160
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor2001101
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins199625
Topology prediction for helical transmembrane proteins at 86% accuracy1996688
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

TwinscanTool Content

http://genes.cs.wustl.edu/ [open in a new window]

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DNA > Gene Prediction

Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measurements between the target sequence and sequences from a closely related genome. Currently sequences from mammalian genomes, and those of Arabidopsis thaliana, C. elegans, C. briggsae and strains JEC21 and H99 of Cryptococcus neoformans can be processed using Twinscan.

links directory index: 526
TitlePublication YearGoogle Scholar Citation Count
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map2003107
Integrating genomic homology into gene structure prediction2001419
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tagsalgorithms animals base composition base sequence chromosome mapping computational biology conserved sequence dna exons forecasting gc rich sequence genes genome human genome humans mice molecular evolution nucleic acid sequence homology predictive value of tests sensitivity and specificity sequence alignment statistical models synteny

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